First of all, EXCELLENT start! Looking really good here. Since the Por15 kit is on the way anyway, just use it to finish up the preparation.
You could get one of those small diameter brush-type attachments, or use a cylindrical sanding attachment, to ream the worst rust out of the tubes, then apply the por15 inside and around the holes.
Jbaj007's advice is good, re. the rust reducer, as an alternative to Por15. I'd wait and read the Por15 directions as far as compatibility. It's likely one or the other will work nicely, since you only have surface rust (and little of that now).
So, having finished the first stage, you now need to examine the finish of the rest of the rocker panel, to plan the blending. Your pics don't show the texture of the surface of the rest of the panel, but it's likely a gentle pebbly effect from a thick coat of whatever compound Mercedes used to undercoat the paint.
I found spray bomb rocker panel coating (not undercoat), like GravelGuard, is fairly close to what my old MB had on it, but yours may differ. You need to find a similar coating to do an effective blend. To make the repairs disappear, and avoid refinishing of the entire panel texture surface, it's essential to get the right stuff under the paint.
Then, it's time to decide whether to repaint the entire panel, or just the repaired areas. You needn't remove weatherstrippng and jack pads, just do a good masking job. If you are going to repaint just the repairs, mask out about 1" beyond the repair, turn the edge of the tape up about 1/4", and spray over/from behind the turned-up edge (like 'over the fence'). This trick helps to avoid a buildup of paint at the masked line. Of course, mask EVERYTHING all around the areas you are working on to minimize overspray.

__________________
1986 560SL
2002 Toyota Camry
1993 Lexus